I've been researching this for 3 weeks and I want to do everything right. This is the last piece of the puzzle. I would like to be able to automate the folder structure/creation for the Drupal sites without removing the ability to add html/php only sites, but it isn't a deal breaker.

If I can get this answered I am going to post my own write up merging all the tutorials into the configuration I implement. Many Druapl developers will benefit from this scenario. Thanks.